This has already been reported in Processing a single Sentinel 2 granule.
From September on S2 data will be distributed as single tiles by default. See Forthcoming Sentinel-2 L1C product evolution in Autumn 2016:
I am having some problems downloading a granule with QGIS SCP, but if you can describe the structure of the product (folders, subfolders, name files…) i will try to help.
I have download a Sentinel 2A iamge with QGIS SCP plug in and in folder I
have all bands and 1 xml file. That is all
the Sentinel-2 reader in SNAP is designed for reading the original SENTINEL-SAFE (see https://sentinel.esa.int/web/sentinel/user-guides/sentinel-2-msi/data-formats ) and that is why the SCP product is not recognized.
But you can open the bands individually (File -> Open product… and select directly the JP2 image files). In this case, to obtain the reflectance you should divide the pixel value by 10000.
That is TOA reflectance without atmospheric correction? By the way is there
option to do atmospheric correction in SNAP?
Yes, the level 1C is TOA reflectance.
As far as i know, with that format it is not possible to launch sen2cor to do the atmospheric correction.
One more last question: I manage to import Sentinel 2A as bands but I am
not sure how I can combine them for example to get vegetation indices?
I am not sure i have understood your question correctly, but i think this will help you:
3 posts were split to a new topic: Open Sen2Cor results in QGIS